An Eight-Parent Multiparent Advanced Generation Inter-Cross Population for Winter-Sown Wheat: Creation, Properties, and Validation

Abstract

MAGIC populations represent one of a new generation of crop genetic mapping resources combining high genetic recombination and diversity. We describe the creation and validation of an eight-parent MAGIC population consisting of 1091 F7 lines of winter-sown wheat (Triticum aestivum L.). Analyses based on genotypes from a 90,000-single nucleotide polymorphism (SNP) array find the population to be well-suited as a platform for fine-mapping quantitative trait loci (QTL) and gene isolation. Patterns of linkage disequilibrium (LD) show the population to be highly recombined; genetic marker diversity among the founders was 74% of that captured in a larger set of 64 wheat varieties, and 54% of SNPs segregating among the 64 lines also segregated among the eight founder lines. In contrast, a commonly used reference bi-parental population had only 54% of the diversity of the 64 varieties with 27% of SNPs segregating. We demonstrate the potential of this MAGIC resource by identifying a highly diagnostic marker for the morphological character "awn presence/absence" and independently validate it in an association-mapping panel. These analyses show this large, diverse, and highly recombined MAGIC population to be a powerful resource for the genetic dissection of target traits in wheat, and it is well-placed to efficiently exploit ongoing advances in phenomics and genomics. Genetic marker and trait data, together with instructions for access to seed, are available at http://www.niab.com/MAGIC/.

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References 35

1. 1.
   Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding · 2013

   No notice
2. 2.

   Bariana H. S. Parry N. Barclay I. R. Loughman R. McLean R. J., 2006 Identification and characterisation of stripe rust resistance gene Yr34 in common wheat. Theor. Appl. Genet. 112: 1143–1148

   Not in our library10.1007/s00122-006-0216-3 (opens in a new tab)

3. 3.

   Bates, D., M. Maechler, B. Bolker, and S. Walker, 2013 lme4: Linear mixed-effects models using Eigen and S4. R package version 1.0–5. http://CRAN.R-project.org/package=lme4/

   Not in our library

4. 4.

   Cavanagh C. Morell M. Mackay I. J. Powell W., 2008 From mutations to MAGIC; resources for gene discovery, validation and delivery in crop plants. Curr. Opin. Plant Biol. 11: 215–221

   Not in our library10.1016/j.pbi.2008.01.002 (opens in a new tab)

5. 5.

   Cavanagh C. R. Chao S. Wang S. Huang B. E. Stephen S., 2013 Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc. Natl. Acad. Sci. USA 110: 8057–8062

   Not in our library10.1073/pnas.1217133110 (opens in a new tab)

6. 6.

   Chanock S. J. Manolio T. Boehnke M. Boerwinkle E. Hunter D. J., 2007 Replicating genotype–phenotype associations. Nature 447: 655–660

   Not in our library10.1038/447655a (opens in a new tab)

7. 7.

   Cockram J. Norris C. O’Sullivan D. M., 2009 PCR markers diagnostic for seasonal growth habit in barley. Crop Sci. 49: 403–410

   Not in our library

8. 8.

   Cockram J. Howells R. M. O’Sullivan D. M., 2010 a Segmental chromosomal duplications harbouring group IV CONSTANS-like genes in cereals. Genome 53: 231–240

   Not in our library10.1139/g09-101 (opens in a new tab)

9. 9.

   Cockram J. White J. Zuluaga D. L. Smith D. Comadran J., 2010 b Genome-wide association mapping to candidate polymorphism resolution in the un-sequenced barley genome. Proc. Natl. Acad. Sci. USA 107: 21611–21616

   Not in our library10.1073/pnas.1010179107 (opens in a new tab)

10. 10.

    Cockram J. Jones H. Norris C. O’Sullivan D. M., 2012 Evaluation of diagnostic molecular markers for DUS phenotypic assessment in the cereal crop, barley (Hordeum vulgare ssp. vulgare L.). Theor. Appl. Genet. 125: 1735–1749

    Not in our library10.1007/s00122-012-1950-3 (opens in a new tab)

11. 11.

    Darvasi A. Soller M., 1995 Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141: 1199–1207

    Not in our library10.1093/genetics/141.3.1199 (opens in a new tab)

12. 12.

    Fulton T. M. Chunwongse J. Tanksley S. D., 1995 Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Mol. Biol. Rep. 13: 207–209

    Not in our library

13. 13.

    Gegas V. C. Gay A. Camargo A. Doonan J. H., 2014 Challenges of crop phenomics in the post-genomics era, pp. 142–171 in Phenomics, edited by Hancock J. M. CRC Press, Boca Raton

    Not in our library

14. 14.

    Hall D. Tegström C. Ingvarsson P. K., 2010 Using association mapping to dissect the genetic basis of complex traits in plants. Brief. Funct. Genomics 9: 157–165

    Not in our library10.1093/bfgp/elp048 (opens in a new tab)

15. 15.

    HGCA, 2012. Protocol CER 12–16. http://www.hgca.com/varieties/recommended-list-protocols.aspx

    Not in our library

16. 16.

    Huang B. E. George A. W., 2011 R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines. Bioinformatics 27: 727–729

    Not in our library10.1093/bioinformatics/btq719 (opens in a new tab)

17. 17.

    Huang B. E. George A. W. Forrest K. L. Killian A. Hayden M. J., 2012 A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotechnol. J. 10: 826–839

    Not in our library10.1111/j.1467-7652.2012.00702.x (opens in a new tab)

18. 18.

    Kato K. Miura H. Akiyama M. Kuroshima M. Sawada S., 1998 RFLP mapping of three major genes, Vrn1, Q and B1, on the long arm of chromosome 5A of wheat. Euphytica 101: 91–95

    Not in our library

19. 19.
    A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana · 2009

    No notice
20. 20.

    Lipka A. E. Tian F. Wang W. Peiffer J. Li M., 2012 GAPIT: Genome Association and Prediction Integrated Tool. Bioinformatics 15: 2307–2399

    Not in our library10.1093/bioinformatics/bts444 (opens in a new tab)

21. 21.

    Luo J. Lui H. Zhou T. Gu B. Huang X., 2013 An-1 encodes a basic helix-loop-xelix protein that regulates awn development, grain size, and grain number in rice. Plant Cell 25: 3360–3376

    Not in our library10.1105/tpc.113.113589 (opens in a new tab)

22. 22.

    Mackay I. Horwell A. Garner J. White J. McKee J., 2011 Reanalyses of the historical series of UK variety trials to quantify the contributions of genetic and environmental factors to trends and variability in yield over time. Theor. Appl. Genet. 122: 225–238

    Not in our library10.1007/s00122-010-1438-y (opens in a new tab)

23. 23.

    Mackay I. J. Powell W., 2007 The significance and relevance of linkage disequilibrium and association mapping in crops. Trends Plant Sci. 12: 57–63

    Not in our library10.1016/j.tplants.2006.12.001 (opens in a new tab)

24. 24.

    Marchini, J. L., 2013 Popgen: Statistical and Population Genetics. R package version 1.0–3. http://CRAN.R-project.org/package=popgen/

    Not in our library

25. 25.

    McIntosh, R. A., G. W. Hart, K. M. Devos, M. D. Gale, and W. J. Rogers, 1998 Catalogue of gene symbols for wheat. Proceedings of the 9th International Wheat Genetics Symposium, Saskatoon, 5: 235.

    Not in our library

26. 26.

    McNeal F. H. Konzak C. F. Smith E. P. Tate W. S. Russel T. S., 1971 A uniform system for recording and processing cereal research data. USDA ARS Bulletin 42: 34–121

    Not in our library

27. 27.
    A method for fine mapping quantitative trait loci in outbred animal stocks · 2000

    Not checked
28. 28.

    Paux E. Sourdille P. Mackay I. Feuillet C., 2012 Sequence-based marker development in wheat: advances and applications to breeding. Biotechnol. Adv. 30: 1071–1088

    Not in our library10.1016/j.biotechadv.2011.09.015 (opens in a new tab)

29. 29.

    Scutari M. Howell P. Balding D. J. Mackay I. J., 2014 Multiple quantitative trait analysis using Bayesian networks. Genetics 198: 129–137

    Not in our library10.1534/genetics.114.165704 (opens in a new tab)

30. 30.

    Snape J. W. Foulkes M. J. Simmonds J. Leverington M. Fish L. J., 2007 Dissecting gene × environmental effects on wheat yields via QTL and physiological analysis. Euphytica 154: 401–408

    Not in our library

31. 31.

    Threadgill D. W. Churchill G. A., 2012 Ten years of the collaborative cross. G3: Genes|Genomes|Genetics 2: 153–155

    Not in our library10.1534/genetics.111.138032 (opens in a new tab)

32. 32.
    Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array · 2014

    No notice
33. 33.

    Watkins A. E. Ellerton S., 1940 Variation and genetics of the awn in Triticum. J. Genet. 40: 243–270

    Not in our library

34. 34.

    White J. Law J. R. MacKay I. Chalmers K. J. Smith J. S. C., 2008 The genetic diversity of UK, US and Australian cultivars of Triticum aestivum measured by DArT markers and considered by genome. Theor. Appl. Genet. 116: 439–453

    Not in our library10.1007/s00122-007-0681-3 (opens in a new tab)

35. 35.

    You T. Yamashita Y. Kanamori H. Matsumoto T. Lundqvist U., 2012 A SHORT INTERNODES (SHI) family transcription factor gene regulates awn elongation and pistil morphology in barley. J Exp Bot 63: 5223–5232

    Not in our library10.1093/jxb/ers182 (opens in a new tab)

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